Comments (7)
In MB I don't know but we regularly train databases with several hundred thousand atoms. Note that with MPI training you can use lots of memory on multiple nodes (or are you already doing that and that's what 1-2 TB refers to?)
from quip.
Just one node , not MPI.
from quip.
So if you switch to multiple nodes you can significantly increase database sizes and reduce training times.
from quip.
Thanks. How do I find how many atoms are in my xyz files?
from quip.
You could load it into ASE and sum the lengths of all the Atoms objects, with something like (not tested)
from ase.io import read
dataset = read("file.xyz", index=":")
total_atoms = sum([len(atoms) for atoms in dataset])
or if you have only a single species eg Si then grep -Ec ‘^Si' file.xyz
would suffice (this counts the number of lines starting with Si).
from quip.
If you have many elements, you can also grep -c 'Lattice' file.xyz
which will count the number of structures, and subtract twice this number from the result of wc file.xyz
to get the overall number of atoms.
from quip.
You can also sum up the atom numbers at the start of each frame/configuration:
grep '^[0-9]\+$' data.xyz | awk '{s+=$1} END {print s}'
Number of frames accordingly:
grep '^[0-9]\+$' data.xyz | wc -l
from quip.
Related Issues (20)
- Added better compatibility for soap_turbo definitions and add_species=T support HOT 2
- RMSE for Liquids in GAP HOT 6
- pip install quippy-ase error HOT 10
- OS/Python version combination (in connection to pip install quippy-ase error #623) HOT 20
- cpu overhead during potential file reading HOT 5
- Compilation Error HOT 5
- Error while reading old trained models and dimer descriptors issue HOT 5
- Regarding Absolute Error of configurations of training set
- fatal error: mach/host_info.h: No such file or directory HOT 4
- Compilation Error HOT 1
- General trimer descriptor and gap_fit HOT 5
- QUIPPY installation issue
- SYSTEM ABORT: Traceback (most recent call last) File "/io/QUIP/src/GAP/gp_predict.f95", line 485 kind unspecified HOT 7
- gap_fit MPI Segmentation fault HOT 20
- Let's have the makefiles cry with very old compiler versions HOT 1
- gap_si_surface.ipynb: runtime error about dftb-params.xml HOT 1
- angle_3b not MPI ready HOT 2
- Empty output file from quip command HOT 37
- SYSTEM ABORT: Database was created with a later version of the code. (in LAMMPS) HOT 2
- LAMMPS + QUIP HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from quip.